Structural deficits in key domains of Shank2 lead to alterations in postsynaptic nanoclusters and to a neurodevelopmental disorder in humans

Abstract

Postsynaptic scaffold proteins such as Shank, PSD-95, Homer and SAPAP/GKAP family members establish the postsynaptic density of glutamatergic synapses through a dense network of molecular interactions. Mutations in SHANK genes are associated with neurodevelopmental disorders including autism and intellectual disability. However, no SHANK missense mutations have been described which interfere with the key functions of Shank proteins believed to be central for synapse formation, such as GKAP binding via the PDZ domain, or Zn2+-dependent multimerization of the SAM domain. We identify two individuals with a neurodevelopmental disorder carrying de novo missense mutations in SHANK2. The p.G643R variant distorts the binding pocket for GKAP in the Shank2 PDZ domain and prevents interaction with Thr(−2) in the canonical PDZ ligand motif of GKAP. The p.L1800W variant severely delays the kinetics of Zn2+-dependent polymerization of the Shank2-SAM domain. Structural analysis shows that Trp1800 dislodges one histidine crucial for Zn2+ binding. The resulting conformational changes block the stacking of helical polymers of SAM domains into sheets through side-by-side contacts, which is a hallmark of Shank proteins, thereby disrupting the highly cooperative assembly process induced by Zn2+. Both variants reduce the postsynaptic targeting of Shank2 in primary cultured neurons and alter glutamatergic synaptic transmission. Super-resolution microscopy shows that both mutants interfere with the formation of postsynaptic nanoclusters. Our data indicate that both the PDZ- and the SAM-mediated interactions of Shank2 contribute to the compaction of postsynaptic protein complexes into nanoclusters, and that deficiencies in this process interfere with normal brain development in humans.

Cryo-electron tomography reveals postsynaptic nanoblocks in excitatory synapses

“…Other postsynaptic proteins situated in the gaps between these nanoblocks may play a role in the regulation and organization of smaller nanoblocks into larger ones. However, considering the diversity of PSD protein complexes [55][56][57][58] , it remains possible that the composition of different-sized PSD nanoblocks varies. Further exploration of the composition of PSD nanoblocks will help us uncover the distinctions and similarities between nanoblocks and nanodomains.…”

Advancements in the study of synaptic plasticity and mitochondrial autophagy relationship

“…PSD-95 is closely associated with processes involving neural development, glutamate transmission, synaptic plasticity, and dendritic spine morphology (Figure 1b). Hassani Nia et al, 2022).…”

“…The Shank family includes three subtypes: Shank1, Shank2, and Shank3, all of which contain multiple structural domains such as ANK, SH3, PDZ, and SAM domains. Shank plays a role in integrating intermediate scaffold proteins in dendritic spines, connecting glutamate receptors to the actin cytoskeleton, and participating in the regulation of neuronal development, axon growth, synaptic formation and stability, and synaptic plasticity (Halbedl et al., 2016; Hassani Nia et al., 2022).…”

Sticky, Adaptable, and Many‐sided: SAM protein versatility in normal and pathological hematopoietic states

“…Nucleus N-terminal Docking site for ERK2 [85] Promotes ETS1 phosphorylation and target gene expression [85] ETS2 Nucleus N-terminal Docking site for ERK2 [85] Promotes ETS2 phosphorylation and target gene expression [85] P63 Cytoplasm C-terminal Binds to GM1 ganglioside [139] P73 Cytoplasm, nucleus C-terminal Binds to lipids [16] GAREM1 Cytoplasm, nucleus C-terminal Intramolecular interaction with CABIT domain [59] SAMHD1 Nucleus, plasma membrane N-terminal Intramolecular interaction with HD domain [144] Intramolecular interaction promotes tetramer formation [144] SAMD14 Cytoplasm C-terminal Promotes PI3K/AKT and MAPK signaling [6] SAMD9l Cytoplasm N-terminal Cell cycle regulation and DNA repair [37] Known SAM containing proteins where in the absence of SAM-SAM interactions, SAM interacts with signaling molecules (ERK2), lipids or promote intramolecular interactions with other domains within the protein.…”

“…SASH3 (SLy1) Cytoplasm, nucleus C-terminal Homodimer [136] Promotes PI3K/AKT and MAPK signaling [98] EPHA3 Plasma membrane C-terminal Homodimer [33] Ligand independent dimerization of SAM [33] Heterodimer Heterodimer with EphA2, ubiquitinated EphA8 [29] Prevents degradation of Eph receptors [29] ARAP3 Cytoplasm, plasma membrane N-terminal Heterodimer with Ship2 [56] EPHA1 Plasma membrane C-terminal Heterodimer with Ship2-SAM, Anks1a-SAM [28] EPHA2 Plasma membrane C-terminal Heterodimer with Ship2-SAM [28 , 29] , Odin-SAM [137] Inhibits EphA2 endocytosis [28] EPHA5 Plasma membrane C-terminal Heterodimer with Samd5 [138] EPHA6 Plasma membrane C-terminal Heterodimer with Ship2-SAM, Anks1a-SAM,Samd5 [4,139] EPHA7 Plasma membrane C-terminal Heterodimer with Samd5 [4] EPHA8 Plasma membrane C-terminal Heterodimer with Anks1a-SAM, Samd5 [4] EPHB1 Plasma membrane C-terminal Heterodimer with Samd5 [4] EPHB2 Plasma membrane C-terminal Heterodimer with Samd5, [4] possible polymer [13] EPHB3 Plasma membrane C-terminal Heterodimer with Samd5 [4] EPHB4 Plasma membrane C-terminal Heterodimer with Samd5 [4] FLI1 Nucleus N-terminal Heterodimer with ETV6 [73] SMBT1 Nucleus C-terminal Heterodimer with Scm-SAM [67] Gene silencing through PRC1 complex [67] SMBT2 Nucleus C-terminal Heterodimer with Scm-SAM [67] Gene silencing through PRC1 complex [67] List of SAM containing proteins with known SAM-dependent homo and heteromeric interactions, with its cellular localization (plasma membrane, nuclear, or cytoplasm), location of the SAM within the protein and known SAM functions.…”